This project is mirrored from https://github.com/Ensembl/format-transcriber.
Pull mirroring updated .
- 19 Feb, 2018 1 commit
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Kieron Taylor authored
Escape curly bracket in regex which fails for new perl versions
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- 04 Dec, 2017 1 commit
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Ridwan Amode authored
escape curly bracket in regex which fails for new perl version
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- 08 Nov, 2017 1 commit
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Magali Ruffier authored
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- 24 Feb, 2017 1 commit
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Magali Ruffier authored
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- 14 Jul, 2016 1 commit
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Matthew Laird authored
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- 05 Jul, 2016 1 commit
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Matthew Laird authored
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- 21 Jun, 2016 3 commits
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Matthew Laird authored
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Matthew Laird authored
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Matthew Laird authored
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- 20 Jun, 2016 2 commits
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Matthew Laird authored
Chromosome mappings updated so species is at a separate level from ucsc_to_ensembl and ensembl_to_ucsc entries
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Matthew Laird authored
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- 15 Jun, 2016 1 commit
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Matthew Laird authored
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- 14 Jun, 2016 1 commit
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Matthew Laird authored
- Add a MeTooDelete callback module that looks backwards if a record has been deleted, and deletes the current record if so - Update the gff3_filter_large example to use MeTooDelete to full clean a GTF/GFF3 record set for large records
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- 09 Jun, 2016 2 commits
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Matthew Laird authored
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Matthew Laird authored
Callback processor to rewrite fasta headers, given a fasta header format regex string and the lookup tables to use for substitution
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- 31 Mar, 2016 1 commit
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Matthew Laird authored
A soft error if an attribute in the configuration file doesn't exist in the gxf file being processed.
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- 30 Mar, 2016 1 commit
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Matthew Laird authored
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- 18 Feb, 2016 1 commit
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Matthew Laird authored
Will likely only work GTF<->GFF3, metadata may not be formatted correctly, and if other format conversions are attempted it will likely explode spectacularly.
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- 03 Feb, 2016 2 commits
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Matthew Laird authored
- Created a GTF parser to enable properly parsing metadata in this format
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Matthew Laird authored
- Added transcript_id filter to mirror gene_id to transcript_id in gene records to make tools such as RNA-SeqC happy with our GTF format - Updated GTF processor to properly format GTF on write with proper delimiters for attributes field - Removed some debugging output left in FileHandle object - Fixed issue where parser object type was being overwritten on the actual parsing of a file
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- 15 Jan, 2016 1 commit
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Matthew Laird authored
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- 13 Jan, 2016 2 commits
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Matthew Laird authored
- Update copyright year
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Matthew Laird authored
- Remapping module and example
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- 12 Jan, 2016 1 commit
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Matthew Laird authored
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- 08 Jan, 2016 1 commit
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Matthew Laird authored
- Metadata is treated like an object for processing - Look-back buffer for the previous written record and the previous processed record
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- 06 Jan, 2016 1 commit
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Matthew Laird authored
- Added a filter callback to do matching, regex and equalities on fields in a record to include or delete that record from the output
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- 05 Jan, 2016 2 commits
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Matthew Laird authored
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Matthew Laird authored
- Created first real filter, to remove padding from sequence type objects - Base configurations for unpadding filter
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- 04 Jan, 2016 5 commits
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Matthew Laird authored
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Matthew Laird authored
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Matthew Laird authored
- Documentation on config format and example config and command lines
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Matthew Laird authored
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Matthew Laird authored
- Don't buffer the output when writing - Dummy callbacks should chatter their debugging data to STDERR rather than STDOUT
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- 21 Dec, 2015 7 commits
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Matthew Laird authored
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Matthew Laird authored
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Matthew Laird authored
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Matthew Laird authored
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Matthew Laird authored
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Matthew Laird authored
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Matthew Laird authored
Turn on coveralls
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